Widespread occurrence of self-cleaving ribozymes

Abstract

Hepatitis delta virus (HDV) and cytoplasmic polyadenylation element-binding protein 3 (CPEB3) ribozymes form a family of self-cleaving RNAs characterized by a conserved nested double-pseudoknot and minimal sequence conservation. Secondary structure-based searches were used to identify sequences capable of forming this fold, and their self-cleavage activity was confirmed in vitro. Active sequences were uncovered in several marine organisms, two nematodes, an arthropod, a bacterium, and an insect virus, often in multiple sequence families and copies. Sequence searches based on identified ribozymes showed that plants, fungi, and a unicellular eukaryote also harbor the ribozymes. In Anopheles gambiae, the ribozymes were found differentially expressed and self-cleaved at basic developmental stages. Our results indicate that HDV-like ribozymes are abundant in nature and suggest that self-cleaving RNAs may play a variety of biological roles.

Fig. 1

A. gambiae drz-Agam-2-1 ribozyme. (A) Core elements are colored by region corresponding to the HDV ribozyme (). Boxed letters are the six invariant positions used in secondary structure searches that identified the ribozymes listed in (B). (C) Graph of in vitro self-cleavage in 1 mM MgCl₂ and (D) RT-qPCR of drz-Agam-2-1 isolated from indicated developmental stages. (Inset) 5′ RACE of the ribozyme. All data are average values ± average deviations.